We have devised a new strategy for the mapping of sites of phosphorylation/dephosphorylation in proteins using enzyme proteolysis in combination with MALDI-ion trap mass spectrometry. The strategy relies on the rapid recognition of peptides that contain sites of phosphorylation by the use of a signature of pairs of peaks separated by 98 Da. The strategy has been used to map sites of phosphorylation/dephosphorylation in a number of different systems including the synapsins and regulation domain of the CFTR chloride channel.